A new comprehensive evaluating system of water quality has been proposed based on the variable weight, which includes a single-factor evaluating method based on percentile system, a determination method for the dynamic factor of weight based on water quality data, and an integrated evaluating method of water quality. This evaluation system is used to carry out the single-factor evaluation, the factor weight calculation and the comprehensive evaluation on the water quality of some stations in Jiangsu province. After that, the correlation analysis on the evaluated results has also been conducted. The results show that the evaluating system of water quality based on variable weight is very suitable for the evaluation of high-frequent monitoring data for the water quality, which not only highlights the direct influence of dramatically changing factor on the evaluated results but also comprehensively reflects the integrated water quality condition.